Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens

Honigfort, D.; Belda-Ferre, P.; White, D.; Sundararajan, K.; Dawood, M.; LeVieux, J.; Moreno, J.; Qi, X.; Metcalfe, K.; Naranbat, D.; Altomare, A.; Thompson, C.; Perez, C.; Lajoie, B.; Kwon, H.; Bhadha, P.; Rammel, T.; Rabalais, J.; Kellinger, M.; Kruglyak, S.; Arslan, S.; Previte, M.

doi:10.1101/2025.10.11.681797

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bioRxiv · 10.1101/2025.10.11.681797

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens

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Abstract

We present a platform that directly sequences single guide RNAs and endogenous 3'UTRs in fixed cells while simultaneously measuring protein abundance and cellular morphology. We demonstrate platform capability by performing optical pooled screening of CRISPR-perturbed lung cancer cells. This approach unites direct in-sample RNA sequencing with complementary phenotypic readouts, enabling comprehensive, scalable, and functional genomics analyses within a single experiment.

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Honigfort, D., Belda-Ferre, P., White, D., Sundararajan, K., Dawood, M., LeVieux, J., Moreno, J., Qi, X., Metcalfe, K., Naranbat, D., Altomare, A., Thompson, C., Perez, C., Lajoie, B., Kwon, H., Bhadha, P., Rammel, T., Rabalais, J., Kellinger, M., Kruglyak, S., Arslan, S., Previte, M.. 2025-10-13. Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens. https://doi.org/10.1101/2025.10.11.681797

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